UNIX/Linux version - Source code only. Requires ANSI C compiler to compile. This can could also be compiled for Windows or MacOS X - 60KB

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Seq-Gen

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

Recompiled for native Mac OS X. The UNIX version can also be compiled under the OS X terminal.

Improved resolution of the automatic seeding of the random number generator by adding some milliseconds to it. Thus runs of Seq-Gen that are less than a second apart will have different seeds. This probably only matters on UNIX machines using scripts to do multiple (short) runs.